Initializing nucleic acids...done.
Applying constraints...done.
Folding single strand...
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 95% [================================================  ] /                     done.
Writing output ct file...done.
Single strand folding complete.
Initializing nucleic acids...done.
Applying SHAPE constraints...done.
Calculating free energies...done.
efn2 complete.
Converting CT file...CT file conversion complete.
/disk1/www/rails/humanrnamap/cli/./main.py:567: DeprecationWarning: Call to deprecated function (or staticmethod) VARNA. (Class has been renamed 'Structure')
  v = VARNA(structure=fold_dbn, sequence=seq)
Output file: /disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/final_image/RUNX1_fold_1.svg

first - Elapsed time since the previous call: 0.00 seconds
first - Current memory usage: 158.08 MB
setup complete - Elapsed time since the previous call: 0.00 seconds
setup complete - Current memory usage: 158.08 MB
config complete - Elapsed time since the previous call: 0.00 seconds
config complete - Current memory usage: 158.08 MB
read annotations - Elapsed time since the previous call: 0.09 seconds
read annotations - Current memory usage: 171.57 MB
Based on canonical annotations, the following gene is in your area of interest: RUNX1(-)
write fasta - Elapsed time since the previous call: 0.13 seconds
write fasta - Current memory usage: 171.57 MB
Length of region: 84 nt.
100.0% of the region's A/C bases included in the filtered DMS dataset. Ideally, this number should be as high as possible for an experimenally-accurate prediction, and over 70% is recommended.
write dat - Elapsed time since the previous call: 0.18 seconds
write dat - Current memory usage: 175.02 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/Fold "/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/fasta/RUNX1.fasta" "/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/ct/RUNX1.ct" --SHAPE "RUNX1.dat"

fold - Elapsed time since the previous call: 0.10 seconds
fold - Current memory usage: 175.02 MB
Running command: /disk1/www/rails/humanrnamap/cli/bin/efn2 "/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/ct/RUNX1.ct" "/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/fold_FE/RUNX1.txt" -sh "RUNX1.dat"

efn2 - Elapsed time since the previous call: 0.41 seconds
efn2 - Current memory usage: 175.02 MB
This region has 1 predicted structures. 5 is the maximum structures visible on the web server. For up to 20 predictions per region, download and run the code locally.
Running command: /disk1/www/rails/humanrnamap/cli/bin/ct2dot "/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/ct/RUNX1.ct" 1 "/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/fold_dbn/RUNX1_temp1.dbn"

ct2dot - Elapsed time since the previous call: 0.02 seconds
ct2dot - Current memory usage: 175.02 MB
['java', '-cp', '/disk1/www/rails/humanrnamap/cli/bin/VARNAv3-93.jar', 'fr.orsay.lri.varna.applications.VARNAcmd', '-sequenceDBN', 'CAUCGGCAUCGGCAUGUCGGCCAUGGGCUCGGCCACGCGCUACCACACCUACCUGCCGCCGCCCUACCCCGGCUCGUCGCAAGC', '-structureDBN', '.....((..((((..(((((....((((.((((.....................))))..))))....)))))..))))...))', '-o', '/disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/final_image/RUNX1_fold_1.svg', '-title', 'RUNX1, -26.9 ± 1.4\n kcal/mol, AUC: 0.791', '-titleSize', '12', '-basesStyle1', 'fill=#ffffff', '-applyBasesStyle1on', '3,5,6,9,11,12,15,16,17,19,20,24,25,26,27,29,31,32,37,39,41,50,54,55,58,61,65,71,72,74,76,77,79,83', '-basesStyle2', 'fill=#00ffff', '-applyBasesStyle2on', '33,4,70,73,10,45,18,56,57', '-basesStyle3', 'fill=#ffff00', '-applyBasesStyle3on', '64,7,78,82,84,21,22,23,28,30,49,52,53,59,60,63', '-basesStyle4', 'fill=#ff0000', '-applyBasesStyle4on', '1,2,66,67,68,69,8,75,13,14,80,81,34,35,36,38,40,42,43,44,46,47,48,51,62']
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Text: 'C', X: 101.5143512554004, Y: 143.83026519658438, Width: 10.5, Height: 8
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Text: 'G', X: 25.838886122127505, Y: 113.42385605090817, Width: 10.5, Height: 8
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Text: 'C', X: 19.038826153797444, Y: 97.29904671495558, Width: 10.5, Height: 8
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Text: 'U', X: 16.66848016059815, Y: 79.9603111334252, Width: 10.5, Height: 8
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Text: 'A', X: 18.89112889599413, Y: 62.60202422795123, Width: 10.5, Height: 8
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Text: 'C', X: 25.55366569908277, Y: 46.41990770874418, Width: 10.5, Height: 8
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Text: 'C', X: 36.19714321267905, Y: 32.5286630520809, Width: 10.5, Height: 8
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Text: 'A', X: 50.08838786934227, Y: 21.88518553848462, Width: 10.5, Height: 8
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Text: 'C', X: 66.27050438854933, Y: 15.222648735395978, Width: 10.5, Height: 8
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Text: 'A', X: 83.62879129402329, Y: 13.0, Width: 10.5, Height: 8
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Text: 'C', X: 100.96752687555379, Y: 15.370345993199294, Width: 10.5, Height: 8
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Text: 'C', X: 117.09233621150626, Y: 22.170405961529354, Width: 10.5, Height: 8
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Text: 'U', X: 130.892465418102, Y: 32.931759295332995, Width: 10.5, Height: 8
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Text: 'A', X: 141.41729568221206, Y: 46.91311257766506, Width: 10.5, Height: 8
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Text: 'C', X: 147.94182642563374, Y: 63.15136341548168, Width: 10.5, Height: 8
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Text: 'C', X: 150.01661680772827, Y: 80.52794353252636, Width: 10.5, Height: 8
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Text: 'U', X: 147.49874535718254, Y: 97.84587109480219, Width: 10.5, Height: 8
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Text: 'G', X: 140.561655085587, Y: 113.91220453642609, Width: 10.5, Height: 8
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Text: 'C', X: 154.70379070931796, Y: 128.05434016015693, Width: 10.5, Height: 8
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Text: 'C', X: 168.8459263330489, Y: 142.196475783888, Width: 10.5, Height: 8
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Text: 'G', X: 182.98806195677986, Y: 156.33861140761883, Width: 10.5, Height: 8
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Text: 'C', X: 200.89608972064428, Y: 161.54341003028821, Width: 10.5, Height: 8
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Text: 'C', X: 210.4416361695391, Y: 177.5643316668818, Width: 10.5, Height: 8
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Text: 'G', X: 206.49441224391097, Y: 195.7908730385966, Width: 10.5, Height: 8
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Text: 'C', X: 212.19963432514191, Y: 214.95986990864253, Width: 10.5, Height: 8
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Text: 'C', X: 217.90485640637286, Y: 234.1288667786887, Width: 10.5, Height: 8
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Text: 'C', X: 223.6100784876038, Y: 253.29786364873462, Width: 10.5, Height: 8
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Text: 'U', X: 239.92018485865054, Y: 259.64060991239205, Width: 10.5, Height: 8
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Text: 'C', X: 249.39711738866106, Y: 339.9397888792133, Width: 10.5, Height: 8
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Text: 'G', X: 255.10234368917702, Y: 359.10878449348326, Width: 10.5, Height: 8
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Text: 'G', X: 260.807569989693, Y: 378.2777801077532, Width: 10.5, Height: 8
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Text: 'C', X: 266.51279629020894, Y: 397.4467757220232, Width: 10.5, Height: 8
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Text: 'U', X: 280.4803713348537, Y: 407.98987049406315, Width: 10.5, Height: 8
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Text: 'C', X: 285.472447677103, Y: 424.76274066565736, Width: 10.5, Height: 8
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Text: 'C', X: 304.7554179313488, Y: 574.3207370244595, Width: 10.5, Height: 8
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Text: '30', X: 140.47404068051776, Y: 191.6035267926514, Width: 18.0, Height: 8
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Text: '40', X: -4.0, Y: 102.58498897803224, Width: 18.0, Height: 8
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Text: '60', X: 226.4296610033764, Y: 174.3378202909804, Width: 18.0, Height: 8
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Text: '84', X: 301.0054179313488, Y: 594.3207370244595, Width: 18.0, Height: 8
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Text: 'RUNX1, -26.9 ± 1.4
 kcal/mol, AUC: 0.791', X: 101.76370523181407, Y: 607.1207370244595, Width: 142.5, Height: 23
Calculated bounding box: (-4.0, 5.0, 340.7453517532127, 607.1207370244595)
Updated viewBox: -9.0 0.0 354.7453517532127 612.1207370244595
Updated SVG: /disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/final_image/RUNX1_fold_final_1.svg
Combined SVG saved as /disk1/www/rails/humanrnamap/public/result/409c2628-4c8d-49d3-8c72-992281172f5a/final_image/RUNX1_fold_final_1.svg
